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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ), 'gf_id' => 'HOM05D001272', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001272' ), 'data_identifier' => 'HOM05D001272', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001272', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p35650' => 'bna', 'A03p00500' => 'bna', 'A03p01290' => 'bna', 'A03p35750' => 'bna', 'A06p40880' => 'bna', 'A09p14030' => 'bna', 'A09p45950' => 'bna', 'Aa31LG10G7850' => 'aar', 'Aa31LG1G21590' => 'aar', 'Aa31LG2G1050' => 'aar', 'Aa31LG2G4890' => 'aar', 'Aa31LG3G2440' => 'aar', 'Aa31LG3G2450' => 'aar', 'Aa31LG3G2460' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3669' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.3796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5882' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5889' => 'aag', 'Actinidia06014' => 'ach', 'Actinidia06015' => 'ach', 'Actinidia08423' => 'ach', 'Actinidia27365' => 'ach', 'Actinidia33733' => 'ach', 'Actinidia36095' => 'ach', 'Ah.08g210770' => 'amhyb', 'Ah.12g051870' => 'amhyb', 'AL2G11170' => 'aly', 'AL3G21220' => 'aly', 'AL5G17240' => 'aly', 'AL5G33650' => 'aly', 'AL6G13140' => 'aly', 'Aqoxy16s005' => 'aox', 'Aqoxy3G02923' => 'aox', 'Aqoxy4G02839' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1N0X92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34TJV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UA83Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.817MDY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93N1T8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AFR9RL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BN59M2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G9V3KM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GCZ0RK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I837JZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L69YUE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MISE4Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P73I1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P80FSF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CPJF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W6NXS0' => 'arhy', 'AT1G63940' => 'ath', 'AT3G09940' => 'ath', 'AT3G27820' => 'ath', 'AT3G52880' => 'ath', 'AT5G03630' => 'ath', 'ATR0661G449' => 'atr', 'ATR0757G106' => 'atr', 'ATR0820G140' => 'atr', 'ATR1091G064' => 'atr', 'Atru.chr6.2320' => 'acertr', 'Atru.chr8.1598' => 'acertr', 'Atru.chr9.2124' => 'acertr', 'AUR62010744' => 'cqu', 'AUR62019721' => 'cqu', 'AUR62019748' => 'cqu', 'AUR62028576' => 'cqu', 'AUR62033530' => 'cqu', 'AUR62035489' => 'cqu', 'BcaB01g00139' => 'bca', 'BcaB01g00335' => 'bca', 'BcaB01g05796' => 'bca', 'BcaB01g05810' => 'bca', 'BcaB02g07806' => 'bca', 'BcaB03g11580' => 'bca', 'BcaB07g30142' => 'bca', 'BcaB07g31535' => 'bca', 'BcaC01g04254' => 'bca', 'BcaC02g10361' => 'bca', 'BcaC03g17491' => 'bca', 'BcaC04g22664' => 'bca', 'BcaC06g30960' => 'bca', 'BcaC06g33782' => 'bca', 'BcaC07g39651' => 'bca', 'BcaC08g44602' => 'bca', 'BolC2t11512H' => 'bol', 'BolC3t12718H' => 'bol', 'BolC3t16613H' => 'bol', 'BolC4t24510H' => 'bol', 'BolC5t33584H' => 'bol', 'BolC6t37258H' => 'bol', 'BolC7t44211H' => 'bol', 'BolC8t50426H' => 'bol', 'BolC9t54589H' => 'bol', 'BraA02t08567Z' => 'bra', 'BraA03t09511Z' => 'bra', 'BraA03t12749Z' => 'bra', 'BraA06t27010Z' => 'bra', 'BraA07t29813Z' => 'bra', 'BraA09t37050Z' => 'bra', 'BraA09t40055Z' => 'bra', 'C02p54490' => 'bna', 'C03p01660' => 'bna', 'C03p43420' => 'bna', 'C04p29760' => 'bna', 'C05p48480' => 'bna', 'C06p20750' => 'bna', 'C07p36990' => 'bna', 'C08p28140' => 'bna', 'C09p16920' => 'bna', 'CAN.G147.5' => 'can', 'CAN.G206.17' => 'can', 'CAN.G396.16' => 'can', 'CAN.G397.7' => 'can', 'CAN.G498.2' => 'can', 'CAN.G532.34' => 'can', 'CAN.G557.4' => 'can', 'CAN.G9.26' => 'can', 'CANSAT11G1039' => 'cansat', 'CANSAT21G0654' => 'cansat', 'CANSAT64G1825' => 'cansat', 'CANSAT80G2400' => 'cansat', 'CARHR047030' => 'chi', 'CARHR149260' => 'chi', 'CARHR162750' => 'chi', 'CARHR209670' => 'chi', 'Carub.0002s0090' => 'cru', 'Carub.0003s0905' => 'cru', 'Carub.0005s0634' => 'cru', 'Carub.0005s1935' => 'cru', 'Carub.0006s0254' => 'cru', 'Ca_06603_v3' => 'car', 'Ca_10948_v3' => 'car', 'Ca_11635_v3' => 'car', 'Ca_17510_v3' => 'car', 'Ca_30003_v3' => 'car', 'CBR_g42037' => 'cbr', 'Cc06_g05490' => 'ccan', 'Cc06_g15110' => 'ccan', 'Cc07_g02030' => 'ccan', 'Cc08_g15200' => 'ccan', 'CDE04G1183' => 'cde', 'CDE04G2512' => 'cde', 'CDE05G3669' => 'cde', 'CDE08G0439' => 'cde', 'CDE12G0558' => 'cde', 'Cfa012237' => 'cfa', 'Cfa016569' => 'cfa', 'Cfa027358' => 'cfa', 'Ciclev10011764m.g' => 'ccl', 'Ciclev10015090m.g' => 'ccl', 'Ciclev10019842m.g' => 'ccl', 'CiPaw.03G009400' => 'cil', 'CiPaw.03G039800' => 'cil', 'CiPaw.09G010400' => 'cil', 'CiPaw.10G007100' => 'cil', 'CiPaw.12G089700' => 'cil', 'ClCG01G002370' => 'cla', 'ClCG04G009870' => 'cla', 'ClCG09G019070' => 'cla', 'ClCG10G006540' => 'cla', 'ClCG10G019180' => 'cla', 'COL.COLO4_08367' => 'col', 'COL.COLO4_09474' => 'col', 'COL.COLO4_29006' => 'col', 'COL.COLO4_29787' => 'col', 'Cpa.g.sc186.12' => 'cpa', 'Cpa.g.sc2231.1' => 'cpa', 'Cpa.g.sc5.56' => 'cpa', 'Cre06.g271200' => 'cre', 'Cre17.g712100' => 'cre', 'CsaV3_3G005990' => 'csa', 'CsaV3_3G037070' => 'csa', 'CsaV3_5G002470' => 'csa', 'CsaV3_5G027310' => 'csa', 'CsaV3_6G040510' => 'csa', 'CSS0006743' => 'camsi', 'CSS0020551' => 'camsi', 'CSS0027614' => 'camsi', 'CSS0030076' => 'camsi', 'CSS0038648' => 'camsi', 'CSS0038910' => 'camsi', 'CSS0040399' => 'camsi', 'CSS0046543' => 'camsi', 'DCAR_005569' => 'dca', 'DCAR_009150' => 'dca', 'DCAR_013373' => 'dca', 'DCAR_015054' => 'dca', 'DCAR_020770' => 'dca', 'Dinv21232' => 'din', 'Dinv31659' => 'din', 'Dinv35080' => 'din', 'Dinv38902' => 'din', 'Duzib068G0070' => 'dzi', 'Duzib093G0374' => 'dzi', 'Duzib106G0192' => 'dzi', 'Duzib128G0632' => 'dzi', 'Duzib128G1474' => 'dzi', 'Duzib147G0699' => 'dzi', 'Duzib205G0044' => 'dzi', 'Duzib268G0127' => 'dzi', 'ECA233G3316' => 'eca', 'ECA238G2435' => 'eca', 'ECA240G0171' => 'eca', 'ECA246G5222' => 'eca', 'ECA248G0295' => 'eca', 'ECA248G1399' => 'eca', 'EL10Ac4g08604' => 'bvu', 'EL10Ac5g12830' => 'bvu', 'EL10Ac6g13724' => 'bvu', 'EL10Ac7g16956' => 'bvu', 'Eucgr.E00656' => 'egr', 'Eucgr.H00132' => 'egr', 'Eucgr.J02215' => 'egr', 'Eucgr.L03133' => 'egr', 'FAN02G0639' => 'fan', 'FAN02G3172' => 'fan', 'FAN04G1180' => 'fan', 'FAN05G0229' => 'fan', 'FAN05G3608' => 'fan', 'FAN05G5727' => 'fan', 'FAN08G2811' => 'fan', 'FAN09G1573' => 'fan', 'FAN09G1627' => 'fan', 'FAN09G2382' => 'fan', 'FAN11G1328' => 'fan', 'FAN13G0903' => 'fan', 'FAN14G0210' => 'fan', 'FAN14G1362' => 'fan', 'FAN16G1375' => 'fan', 'FAN18G1124' => 'fan', 'FAN21G2602' => 'fan', 'FAN25G2351' => 'fan', 'FvH4_3g20880' => 'fve', 'FvH4_5g03130' => 'fve', 'FvH4_6g18190' => 'fve', 'FvH4_6g50920' => 'fve', 'Glyma.05G211502' => 'gma', 'Glyma.08G017800' => 'gma', 'Glyma.10G067500' => 'gma', 'Glyma.16G073100' => 'gma', 'Glyma.19G061200' => 'gma', 'Glyma.U031121' => 'gma', 'Gohir.A01G207800' => 'ghi', 'Gohir.A09G027000' => 'ghi', 'Gohir.A09G137900' => 'ghi', 'Gohir.A10G103200' => 'ghi', 'Gohir.A12G233700' => 'ghi', 'Gohir.A13G144000' => 'ghi', 'Gohir.D01G197200' => 'ghi', 'Gohir.D09G026700' => 'ghi', 'Gohir.D09G136700' => 'ghi', 'Gohir.D10G087366' => 'ghi', 'Gohir.D12G233700' => 'ghi', 'Gohir.D13G148800' => 'ghi', 'Gorai.002G241300' => 'gra', 'Gorai.006G030700' => 'gra', 'Gorai.006G156800' => 'gra', 'Gorai.008G250000' => 'gra', 'Gorai.011G095600' => 'gra', 'Gorai.013G166500' => 'gra', 'GSVIVG01019412001' => 'vvi', 'GSVIVG01032453001' => 'vvi', 'GSVIVG01033815001' => 'vvi', 'HanXRQChr03g0085961' => 'han', 'HanXRQChr07g0198871' => 'han', 'HanXRQChr12g0377281' => 'han', 'HanXRQChr14g0450411' => 'han', 'HanXRQChr15g0475021' => 'han', 'Haze_08764' => 'cav', 'Haze_08767' => 'cav', 'Haze_14691' => 'cav', 'Haze_19566' => 'cav', 'Hma1.2p1_0084F.1_g043420' => 'hma', 'Hma1.2p1_0216F.1_g091010' => 'hma', 'Hma1.2p1_0216F.1_g091020' => 'hma', 'Hma1.2p1_0232F.1_g097680' => 'hma', 'Hma1.2p1_0232F.1_g097700' => 'hma', 'Hma1.2p1_0858F.1_g229280' => 'hma', 'Hma1.2p1_2385F.1_g321130' => 'hma', 'HPP92_006423' => 'vpl', 'HPP92_008308' => 'vpl', 'HPP92_011516' => 'vpl', 'HPP92_013805' => 'vpl', 'Hund02258' => 'sun', 'Hund04022' => 'sun', 'Hund14276' => 'sun', 'Hund19964' => 'sun', 'Lalb_Chr02g0155091' => 'lal', 'Lalb_Chr05g0224521' => 'lal', 'Lalb_Chr06g0175921' => 'lal', 'Lalb_Chr21g0319521' => 'lal', 'Lalb_Chr25g0288551' => 'lal', 'Lj1g0015063' => 'lja', 'Lj2C132T3' => 'lonja', 'Lj3A1001T32' => 'lonja', 'Lj4g0020327' => 'lja', 'Lj5g0025207' => 'lja', 'Lj8A216T74' => 'lonja', 'Lju41C36G22' => 'lonja', 'Lju41C36G23' => 'lonja', 'Lsat_1_v5_gn_0_28220' => 'lsa', 'Lsat_1_v5_gn_1_48501' => 'lsa', 'Lsat_1_v5_gn_2_91720' => 'lsa', 'Lsat_1_v5_gn_6_64280' => 'lsa', 'Lsat_1_v5_gn_6_85001' => 'lsa', 'Manes.01G057400' => 'mes', 'Manes.08G023066' => 'mes', 'Manes.09G058561' => 'mes', 'Manes.15G149700' => 'mes', 'Mapoly0001s0099' => 'mpo', 'Mapoly0006s0270' => 'mpo', 'Mapoly0057s0016' => 'mpo', 'MBI10_g28016_MAGBIO' => 'mbi', 'MBI17_g38600_MAGBIO' => 'mbi', 'MCO13G286' => 'mco', 'MD09G1030800' => 'mdo', 'MD11G1237900' => 'mdo', 'MD12G1021900' => 'mdo', 'MD14G1018700' => 'mdo', 'MD14G1111300' => 'mdo', 'MD17G1032700' => 'mdo', 'Medtr1g060620' => 'mtr', 'Medtr7g034715' => 'mtr', 'Medtr8g098910' => 'mtr', 'MELO3C005708.2' => 'cme', 'MELO3C009453.2' => 'cme', 'MELO3C016551.2' => 'cme', 'MELO3C021554.2' => 'cme', 'MELO3C024527.2' => 'cme', 'MELO3C034376.2' => 'cme', 'Migut.A00725' => 'egut', 'Migut.H00103' => 'egut', 'Migut.J00970' => 'egut', 'Migut.K01379' => 'egut', 'MSTRG.13858' => 'ama', 'MSTRG.1844' => 'ama', 'MSTRG.19243' => 'ama', 'MSTRG.24026' => 'ama', 'MSTRG.5820' => 'ama', 'Nitab4.5_0001977g0040' => 'nta', 'Nitab4.5_0003015g0030' => 'nta', 'Nitab4.5_0004051g0060' => 'nta', 'Nitab4.5_0008556g0020' => 'nta', 'Nitab4.5_0009062g0020' => 'nta', 'Nitab4.5_0009459g0010' => 'nta', 'Nn1g01649' => 'nnu', 'Nn2g14068' => 'nnu', 'Nn4g22749' => 'nnu', 'Nn6g34998' => 'nnu', 'Oeu003252.1' => 'oeu', 'Oeu009901.1' => 'oeu', 'Oeu018733.1' => 'oeu', 'Oeu042355.1' => 'oeu', 'Oeu048644.1' => 'oeu', 'Oeu052887.2' => 'oeu', 'Oeu054689.1' => 'oeu', 'Oeu056907.1' => 'oeu', 'Os02g0707000' => 'osa', 'Os02g0707100' => 'osa', 'Os08g0151800' => 'osa', 'Os08g0557600' => 'osa', 'Os09g0567300' => 'osa', 'Peaxi162Scf00074g01819' => 'pax', 'Peaxi162Scf00129g10129' => 'pax', 'Peaxi162Scf00290g00059' => 'pax', 'PGR042G0751' => 'pgr', 'PGR083G0697' => 'pgr', 'PGR142G4101' => 'pgr', 'PGSC0003DMG400000486' => 'stu', 'PGSC0003DMG400002703' => 'stu', 'PGSC0003DMG400012322' => 'stu', 'Phvul.002G292800' => 'pvu', 'Phvul.007G230300' => 'pvu', 'Phvul.008G155600' => 'pvu', 'Potri.001G099600' => 'ptr', 'Potri.001G346200' => 'ptr', 'Potri.006G114800' => 'ptr', 'Pp3c14_26470' => 'ppa', 'Pp3c15_710' => 'ppa', 'Pp3c17_22620' => 'ppa', 'Pp3c2_8410' => 'ppa', 'Pp3c9_450' => 'ppa', 'Prupe.3G286700' => 'ppe', 'Prupe.4G189300' => 'ppe', 'Prupe.5G106000' => 'ppe', 'Prupe.6G160700' => 'ppe', 'Prupe.7G114800' => 'ppe', 'Psat3g183240' => 'psa', 'Psat6g083320' => 'psa', 'Psat7g030360' => 'psa', 'PSO063G0795' => 'pso', 'PSO063G6158' => 'pso', 'PSO170G3348' => 'pso', 'PSO339G3126' => 'pso', 'PSO384G2499' => 'pso', 'PSO832G1764' => 'pso', 'QL02p075942' => 'qlo', 'QL07p039808' => 'qlo', 'QL07p040377' => 'qlo', 'QL12p031896' => 'qlo', 'RcHm_v2.0_Chr2g0172301' => 'rch', 'RcHm_v2.0_Chr3g0472521' => 'rch', 'RcHm_v2.0_Chr5g0035251' => 'rch', 'RcHm_v2.0_Chr7g0196651' => 'rch', 'Rhsim03G0078300' => 'rsi', 'Rhsim07G0087700' => 'rsi', 'Rhsim10G0019900' => 'rsi', 'RhsimUnG0166800' => 'rsi', 'Sabra01G0074700' => 'sbr', 'Sabra06G0089700' => 'sbr', 'Sabra16G0225300' => 'sbr', 'Sabra16G0226000' => 'sbr', 'SalBow3G3841' => 'sbo', 'SalBow7G0523' => 'sbo', 'SalBow8G3189' => 'sbo', 'Sc01g0009800' => 'sci', 'Sc02g0001040' => 'sci', 'Sc03g0011040' => 'sci', 'Sc07g0005460' => 'sci', 'Sed0006187' => 'sed', 'Sed0010496' => 'sed', 'Sed0011084' => 'sed', 'Sed0016233' => 'sed', 'Sed0019765' => 'sed', 'Sed0023732' => 'sed', 'SEGI_06648' => 'sgi', 'SEGI_39994' => 'sgi', 'SEGI_40440' => 'sgi', 'SGA_v2.0_scaffold184G39952' => 'sas', 'SGA_v2.0_scaffold30G12444' => 'sas', 'SGA_v2.0_scaffold521G52695' => 'sas', 'SGA_v2.0_scaffold75G24766' => 'sas', 'SHI25722' => 'shi', 'SHI25725' => 'shi', 'SMO118G0072' => 'smo', 'SMO118G0131' => 'smo', 'SMO118G0307' => 'smo', 'Solyc02g086710.3' => 'sly', 'Solyc08g081530.3' => 'sly', 'Solyc09g009390.3' => 'sly', 'Sopen02g031480' => 'spe', 'Sopen08g029850' => 'spe', 'Sopen09g004130' => 'spe', 'Sp2g00750' => 'spa', 'Sp2g16880' => 'spa', 'Sp5g09460' => 'spa', 'Sp6g39120' => 'spa', 'TAR369G0721' => 'tar', 'TAR375G0428' => 'tar', 'TAR622G0219' => 'tar', 'TAR623G1418' => 'tar', 'THA.LOC104809369' => 'tha', 'THA.LOC104816363' => 'tha', 'THA.LOC104823486' => 'tha', 'THA.LOC104823945' => 'tha', 'Thecc.03G285900' => 'tca', 'Thecc.04G011700' => 'tca', 'Thecc.05G084900' => 'tca', 'Thecc.07G072000' => 'tca', 'Thhalv10004089m.g' => 'esa', 'Thhalv10010391m.g' => 'esa', 'Thhalv10013480m.g' => 'esa', 'Thhalv10015502m.g' => 'esa', 'Thhalv10015647m.g' => 'esa', 'Thhalv10015763m.g' => 'esa', 'Thhalv10023425m.g' => 'esa', 'TPR.G12899' => 'tpr', 'TPR.G15230' => 'tpr', 'TPR.G32589' => 'tpr', 'TPR.G5705' => 'tpr', 'TPR.G80' => 'tpr', 'TWI36G1590' => 'twi', 'TWI53G0725' => 'twi', 'TWI74G1646' => 'twi', 'unitig_22.g5120' => 'ugi', 'unitig_26.g9249' => 'ugi', 'unitig_62.g23353' => 'ugi', 'unitig_748.g7425' => 'ugi', 'unitig_749.g14293' => 'ugi', 'vmacro05839' => 'vma', 'vmacro07389' => 'vma', 'vmacro13971' => 'vma', 'VMungo0251G0481' => 'vmu', 'VMungo0251G0543' => 'vmu', 'VMungo0720G2822' => 'vmu', 'VMungo1383G1230' => 'vmu', 'Zm00001eb048070' => 'zma', 'Zm00001eb096070' => 'zma', 'Zm00001eb176160' => 'zma', 'Zm00001eb252200' => 'zma', 'Zm00001eb252210' => 'zma', 'Zm00001eb416430' => 'zma' ) $gf_id = 'HOM05D001272' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001272' ) $data_identifier = 'HOM05D001272' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 7, 'aag' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 16, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 8, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416430' $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